Highly ordered TiO2 nanotubes with large surface-volume ratios were prepared by anodic oxidation, and the effects of annealing in different atmospheres on their structural, optical and magnetic properties were studied. The as-prepared, air and argon annealed samples all showed low-field ferromagnetism and high-field diamagnetism at room temperature. The unexpected decrease in the band-gap and the enhancement of ferromagnetism in the air-annealed sample provide convincing evidence for the morphology dependence. With decreasing test temperature, low-field ferromagnetism gradually increased, and interestingly, the high-field diamagnetism gradually changed to paramagnetism. Moreover, the argon-annealed sample exhibited significantly enhanced ferromagnetism, which varied with the annealing temperature, reaching a maximum at 400 °C. Important effects of the annealing conditions and the induced morphology changes on the optical and magnetic behavior of the nanotubes were revealed, and the origin of ferromagnetism was explained from a new perspective of hydrogen-like impurities based on the characteristics of localized states associated with oxygen vacancies. Our research will be helpful in expanding the application of TiO2 nanotubes.